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SARS-CoV-2: It's All "Omicron"

Information and resources on SARS-CoV-2 (the virus that causes COVID-19)

What is Omicron?

A Brief History of Omicron
The birth of a new Greek Letter Variant

It was 26 November 2021 that WHO declared that the world was facing a new variant of concern: Omicron. It would go on to change the trajectory of the COVID-19 pandemic.

Omicron was quickly identified as being significantly more transmissible than Delta, the preceding variant of concern. Within 4 weeks, as the Omicron wave travelled around the world, it replaced Delta as the dominant variant. By March 2022, WHO and partners estimate that almost 90% of the global population had antibodies against the COVID-19 virus, whether through vaccination or infection.

Since the emergence of Omicron, the virus has continued to evolve. Today, there are over [1,000] sublineages of this variant circulating, but not one has been designated as a new variant of concern. So far, these sublineages of Omicron have much in common: they are all highly transmissible, replicate in the upper respiratory tract and tend to cause less severe disease compared to previous variants of concern, and they all have mutations that make them escape built-up immunity more easily. This means that they are similar in their impact on public health, and the response that is needed to deal with them.

If the virus were to change significantly – like if a new variant caused more severe disease, or if vaccines no longer prevented severe disease and death – the world would need to reconsider its response. In that case, we would have a new variant of concern, and with it, new recommendations and strategy from WHO.

From: WHO, One year since the emergence of COVID-19 virus variant Omicron, 25 Nov 2022


"Variant Soup"

Beginning in late 2020 (after the initial COVID-19 global surge in Spring-Summer 2020), there have been distinct waves caused by each of the "Variants of Concern (VOC)": Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617), and Epsilon (B.1.427/B.1.429). After the Delta wave subsided in late 2021, the newly named Omicron (B.1.1.529) began to quickly spread across the globe.

However, unlike previous variants that quickly took dominance over other variants, Omicron quickly mutated and began co-circulating with its own subvariants. This led to "variant soup", where not one single variant/subvariant could claim dominance over all the others. It also led to sustained high viral transmission levels instead of the wave-like ebb and flow that was characteristic of previous variants. Instead of waves that were concerning, it became the "area under the curve" that was causing problems. That is, while there were no huge surges after the initial Omicron (BA.1) surge in January 2022, there was instead sustained high transmission that never subsides. This is actually more alarming, as it does not give healthcare systems any break.

What was even more concerning was the increasing number of reinfection (infection after previous COVID-19 infection) and breakthrough infection (infection after COVID-19 vaccination). Since many of these Omicron subvariants have the ability to escape the immune system, COVID-19 vaccines no longer can prevent infection (though they still protect against severe illness, hospitalization, and death!!), and individuals can become reinfected with different subvariants within weeks or months of previous infection.


Omicron "Nicknames"

By mid-2022, the situation with variant evolution had become considerably more complex, with hundreds of (sub)variants identified, all of them falling within “Omicron”. This meant that discussions of the most important variants have only two formal naming options: WHO Greek letters (which is all currently “Omicron”) or an increasingly complex collection of PANGO lineages (in many cases now several layers of “aliases” deep) (World Health Network, 2023).

SARS-CoV-2 variant trackers began to identify the most concerning subvariants with informal "nicknames". In September 2021, the subvariant BA.4.6 became the first Omicron variant with a nickname, "Aeterna". Since then almost two-dozen Omicron subvariants have been given informal nicknames based on Greek mythological creatures.


"Common Names"

In early 2023 a new proposal for consistent assignment of "common names" to variants was established, with the purpose of:

facilitate broader communication, to reduce confusion, and to accurately reflect the state of ongoing variant evolution of SARS-CoV-2, and identify new variants of potential concern to help communicate about public health guidance and policy (e.g., recommendations for mitigation measures, effectiveness of vaccines and treatments).

The newly proposed naming system has chosen a naming structure drawn from astronomy (constellations, stars, moons, asteroids, exoplanets).

The first variant to receive a nickname using the new system was XBB.1.9.1 "Hyperion", after a moon of Saturn. XBB.1.9.1 (Hyperion) is the 1st descendant of the 9th descendant of the first descendant of XBB. It is not descended from XBB.1.5 (Kraken).


WHO Updates Variant Definitions

On 15 March 2023, WHO updated its tracking system and working definitions for variants of SARS-CoV-2, the virus that causes COVID-19, to better correspond to the current global variant landscape, to independently evaluate Omicron sublineages in circulation, and classify new variants more clearly when required.

With these changes factored in, Alpha, Beta, Gamma, Delta as well as the Omicron parent lineage (B.1.1.529) are considered previously circulating VOCs. WHO has now classified XBB.1.5 as a VOI. 

WHO emphasizes that these changes do not imply that the circulation of Omicron viruses no longer pose a threat to public health. Rather, the changes have been made in order to better identify additional or new threats over and above those posed by the current Omicron viruses in circulation.


List of All Omicron (Sub)Lineages

covSPECTRUM Collection #71 - Maintained by @alurqu

Designated Omicron lineages including recombinant lineages involving Omicron (including Omicron-Omicron and Delta-Omicron recombinants).

Omicron Parent Lineages

These are the originating Omicron lineages that all current variants and sub-variants descend from. See Omicron Evolution for more details on each of these descendants.

Pango Lineage Alias
BA.1 B.1.1.529.1
BA.2 B.1.1.529.2
BA.3* B.1.1.529.3
BA.4 B.1.1.529.4
BA.5 B.1.1.529.5

*BA.3 occurred very infrequently and to date has no descendant lineages

Omicron "Nicknames"

Since Omicron first appeared in late 2021, there have been over 1,000 distinct of Omicron subvariants identified. Below are the ones that have gained such significant traction that they have been given informal "nicknames" to make it easier to distinguish between them.

Omicron Nicknames [Legacy**]

Nickname Pango Name Sublineage(s) Omicron Ancestry Identified/Named
"Omicron OG" BA.1

BA.1 (B.1.1.529.1)

BA.1 November 2021, South Africa
"Stealth Omicron" BA.2

BA.2 (B.1.1.529.2)

BA.2 January 2022
"Aeterna" BA.4.6 BA.4 BA.4 September 2022
"Argus" BJ.1 BA.2 BA.2 September 2022
"Basilik" BA.2.3.20 BA.2 BA.2 September 2022
"Bythos" XBF* BA.5.2 & CJ.1

BA.5 & BA.2

December 2022, Australia
"Centaurus" BA.2.75 BA.2 BA.2 August 2022
"Cerberus" BQ.1.1 BQ.1 BA.5 October 2022
"Cerastes" BR.2.1 BA.2.75 BA.2 December 2022
"Cetus" BA.4.1.9 BA.4 BA.4 August 2022
"Chiron" BA.2.75.2 BA.2.75 BA.2 September 2022
"Dictys" BA.2.75.6 BA.2.75 BA.2 September 2022
"Gryphon" XBB* BJ.1 & BM1.1.1 BA.2 & BA.2 October 2022
"Hippogryph" XBB.1* XBB [BJ.1/BM1.1.1] BA.2 & BA.2 November 2022
"Hydra" BN.1 BA.2.75 BA.2 November 2022
"Kraken" XBB.1.5 XBB [BJ.1/BM1.1.1] BA.2 & BA.2

December 2022, US (NY)

"Mimas" BM.1.1.1 BA.2 BA.2 September 2022
"Minotaur" BF.7 BA.4 BA.4 September 2022
"Orthos" CH.1.1 BA.2.75 BA.2 October 2022, UK
"Pallas" BA.5.2.48 BA.5.2 BA.5 January 2023, China*
"Python" BF.11 BA.5.2 BA.5 November 2022
"Sphinx" BA.5.1 BA.5 BA.5 August 2022
"Tarandos" BF.7.14 BF.7 BA.5 January 2023, China*
"Triton" BA.5.2 BA.5 BA.5 August 2022
"Typhon" BQ.1 BA.5 BA.5 October 2022

Nicknames: T. Ryan Gregory @TRyanGregory

*Chinese-originated variants, likely little global spread due to lack of immune-evasiveness.

SARS-CoV-2 "Common Names"

SARS-CoV-2 Variant "Common Names"

On February 18, 2023 @TRyanGregory announced a proposed new "Common Names" for Notable SARS-CoV-2 Variants naming system based on astronomy. Starting letter indicates lineage/genetic background, a letter "R" in the name shows recombinant ancestry.

  1. Names beginning with letters A-H are used for members of the BA.2 lineage.
  2. Names beginning with letters I-J are used for the BA.4 lineage.
  3. Names beginning with letters K-T are used for the BA.5 lineage.
  4. Names beginning with letters U-Z are used for miscellaneous or mixed lineage variants.
  5. Within the above, names that contain the letter R are used for variants that are recombinants or descendants of recombinants.

The first variant to receive a nickname using the new system is XBB.1.9.1 "Hyperion", after a moon of Saturn. XBB.1.9.1 (Hyperion) is the 1st descendant of the 9th descendant of the first descendant of XBB. It is not descended from XBB.1.5 (Kraken).

**Legacy nicknames using Greek mythological creatures obviously don't follow the updated nomenclature rules and it will be made clear which ones those are.


Assigned SARS-CoV-2 Variant Common Names
Common Name PANGO Name Sublineage(s) Recombinant (Y/N) Ancestry
"Hyperion" XBB.1.9.1 XBB* [BJ.1/BM.1.1.1] Yes BA.2
"Arcturus" XBB.1.16 XBB* [BJ.1/BM.1.1.1] Yes BA.2
"Acrux" XBB.2.3* XBB* [BJ.1/BM.1.1.1] Yes BA.2
"Bellatrix" FY.4* XBB.1.22.1 Yes BA.2
"Eris" EG.5.1 XBB.1.9.2 Yes BA.2
"Fornax" FL.1.5.1 XBB.1.9.1 Yes BA.2
"Pirola" BA.2.86 B.1.1.529.2* [BA.2] No BA.2